comparison drmutations.xml @ 0:71976cfc9022 draft

planemo upload for repository https://github.com/phac-nml/quasitools commit 8a264400a75945e2e0fdd5a08c007a8b1b7a2f0f
author nml
date Mon, 04 Dec 2017 10:25:26 -0500
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children a7093d5933a8
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-1:000000000000 0:71976cfc9022
1 <tool id="drmutations" name="Drug Resistance Mutations" version="0.1.0">
2 <description></description>
3 <requirements>
4 <requirement type="package" version="0.2.2">quasitools</requirement>
5 </requirements>
6 <command detect_errors="exit_code"><![CDATA[
7
8 ln -f -s ${input_bam.metadata.bam_index} ${input_bam}.bai &&
9 quasitools drmutations $input_bam $ref_file $var_file $input_genes
10
11 #if $mutation_db:
12 $mutation_db
13 #end if
14
15 #if $min_freq:
16 -f $min_freq
17 #end if
18
19 #if $reporting_thres:
20 -t $reporting_thres
21 #end if
22
23 -o output.csv
24
25 ]]></command>
26 <inputs>
27 <param name="input_bam" type="data" format="bam" optional="false" label="Bam file" />
28 <param name="ref_file" type="data" format="fasta" optional="false" label="Reference file" />
29 <param name="var_file" type="data" format="vcf" optional="false" label="Variants file" />
30 <param name="input_genes" type="data" format="bed" optional="false" label="Gene file" />
31 <param name="mutation_db" type="data" format="tsv" optional="false" label="Mutation DB" />
32 <param name="min_freq" type="float" optional="true" min="0" max="1" label="Minimum frequency" value="0.01" help="The minimum required frequency. Defaults to 0.01." />
33 <param name="reporting_thres" type="integer" min="1" max="20" optional="true" label="Reporting threshold" value="1"
34 help="The minimum percentage required for an entry in the drug resistant report. Defaults to 1."/>
35 </inputs>
36 <outputs>
37 <data format="csv" name="output" from_work_dir="output.csv" />
38 </outputs>
39 <tests>
40 <test>
41 <param name="input_bam" value="align.bam" />
42 <param name="ref_file" value="hxb2_pol.fas" />
43 <param name="var_file" value="nt_variants.vcf" />
44 <param name="input_genes" ftype="bed" value="hxb2_pol.bed" />
45 <param name="mutation_db" value="mutation_db.tsv" />
46 <output name="output" >
47 <assert_contents>
48 <has_text text="Chromosome,Gene,Category,Surveillance,Wildtype,Position,Mutation,Mutation Frequency,Coverage" />
49 <has_text text="hxb2_pol,RT,NNRTI,Yes,K,103,N,7.79,154" />
50 </assert_contents>
51 </output>
52 </test>
53 </tests>
54 <help><![CDATA[
55
56 Drug Resistance Mutations
57 =========================
58
59 Generates a report detailing the drug resistant mutations found, above the reporting threshold (default: 1%).
60
61 ]]></help>
62 <citations>
63 </citations>
64 </tool>